Two paraoxonase (PON1) polymorphisms, PON1-Q192R and PON1-L55M have been inconsistently associated with vascular disease. However, plasma PON1 activity phenotypes vary markedly within genotypes. Thus, activity was expected to add to the informativeness of genotype for predicting vascular disease. The case-control study included 212 age and race matched men with mean age 66.4 yr. (range 49-82 yr.); 95% were Caucasian. The 106 carotid artery disease (CAAD) cases had >80% carotid stenosis and the 106 controls had <15% stenosis. Two PON1 substrate hydrolysis rates (paraoxon, POase; diazoxon, DZOase) were significantly lower in cases than in controls and were significant predictors of CAAD using logistic regression (POase, p=0.005, 25% reduced; DZOase, p=0.019, 16% reduced). POase and DZOase were both significant when included in the same model. DZOase predicted vascular disease independently of lipoprotein profile, HDL subfractions, apoAI, and smoking. The marginal effects of PON1-192 (p=0.75) and PON1-55 (p=0.83) genotypes or haplotype (0.70) did not predict case-control status. However, when phenotype was included as a predictor both PON1-192 and PON1-55 genotypes or haplotypes were significant predictors at the 0.05 level. The common methodology of examining PON1-192 and/or PON1-55 genotypes alone may lead to the erroneous conclusion that there is no PON1 role in CAAD. This may have broad implications for the utility of the "genotype only" approach. These results support the benefit of a "level crossing" approach that includes intervening phenotypes in the study of complexly inherited disease